Endoderm cells of the ascidian embryo are specified autonomously dependent on maternal cytoplasmic information or determinants that are localized in the endoplasm. In the present study, we identified three maternally expressed genes (CsEndo-1, CsEndo-2 and CsEndo-3) by screening a cDNA library of Ciona savignyi fertilized egg mRNAs subtracted with gastrula mRNAs. CsEndo-1 encoded a protein with nuclear localization signals, CsEndo-3 predicted a protein containing both a potential transmembrane domain and the PDZ domain, and CsEndo-2 suggested a protein with no similarity to known proteins. The maternal transcripts of all of these genes were not concentrated during early stages of embryogenesis up to the 8-cell stage, but were concentrated at the endoplasmic region by the 16-cell stage and then segregated later with the endoplasm. At the 110-cell stage, the maternal transcript of CsEndo-1 was evident only in the primordial endoderm cells, while those of CsEndo-2 and CsEndo-3 were found in the primordial endoderm cells as well as the primordial notochord cells. All of the transcripts became barely detectable during gastrulation and neurulation. Later, zygotic expression of the three genes became evident again in the endoderm and notochord cells, suggesting developmental roles in the formation of these types of cell. Although we were not able to deduce their functions, this is the first report of maternal genes with mRNAs that are segregated with the endoplasm of ascidian embryos.